A new alligatoroid from the Eocene of Vietnam highlights an extinct Asian clade independent from extant Alligator sinensis

Expanded phylogeny elucidates Deinosuchus relationships, crocodylian osmoregulation and body-size evolution

Transmarine distribution and gigantism in the Late Cretaceous North American crocodyliform Deinosuchus has been difficult to reconcile with consistently inferred phylogenetic relationships to alligatorids, an otherwise freshwater and smaller-bodied group. We present an expanded phylogeny with increased spatiotemporally coherence that reinterprets species of Deinosuchus as stem-group crocodylians together with further putative alligatoroids, Leidyosuchus canadensis and the European Diplocynodon spp. (closely related to North American Borealosuchus). The novel topology elucidates the evolution of osmoregulation in Crocodylia and its close relatives by inferring plesiomorphic saltwater tolerance for Deinosuchus and the crown-group as well as secondary loss already in stem-group alligatorids. Divergence of Alligatoroidea coincided with extreme mid-Cretaceous sea level highs and the distribution of Deinosuchus across the Western Interior Seaway can be best explained by marine dispersal. Phylogenetic body-length analysis using a head-width proxy reveals phyletic dwarfism early in alligatoroid evolution and a reasonable total length estimate for the most complete specimen of Deinosuchus riograndensis. We find that gigantism in crocodyliforms is correlated with high-productive extensive aquatic ecosystems in the present and the past.

The biogeographic history of neosuchian crocodiles and the impact of saltwater tolerance variability

Extant neosuchian crocodiles are represented by only 24 taxa that are confined to the tropics and subtropics. However, at other intervals during their 200 Myr evolutionary history the clade reached considerably higher levels of species-richness, matched by more widespread distributions. Neosuchians have occupied numerous habitats and niches, ranging from dwarf riverine forms to large marine predators. Despite numerous previous studies, several unsolved questions remain with respect to their biogeographic history, including the geographical origins of major groups, e.g. Eusuchia and Neosuchia itself. We carried out the most comprehensive biogeographic analysis of Neosuchia to date, based on a multivariate K-means clustering approach followed by the application of two ancestral area estimation methods (BioGeoBEARS and Bayesian ancestral location estimation) applied to two recently published phylogenies. Our results place the origin of Neosuchia in northwestern Pangaea, with subsequent radiations into Gondwana. Eusuchia probably emerged in the European archipelago during the Late Jurassic/Early Cretaceous, followed by dispersals to the North American and Asian landmasses. We show that putative transoceanic dispersal events are statistically significantly less likely to happen in alligatoroids. This finding is consistent with the saltwater intolerant physiology of extant alligatoroids, bolstering inferences of such intolerance in their ancestral lineages.

Exceptionally well-preserved crocodilian coprolites from the Late Eocene of Northern Vietnam: Ichnology and paleoecological significance

This study examines 55 coprolites from the Na Duong Basin to reconstruct the paleoenvironment. Coproecology sheds light on understanding the complex prey-predator relationships, trophic dynamics, and ecosystem evolution. Through quantitative and multidisciplinary analysis, the putative coprolites were attributed to crocodilian producers, leading to the establishment of a new ichnogenus and species, Crococopros naduongensis igen. et isp. nov., based on distinct characteristics and comparisons. The study provides compelling evidence of an ancient river or lake-like environment dominated by diverse crocodilian fauna, indicating a thriving food chain in the Na Duong Basin. The findings also highlight the remarkable richness of ichnofauna, fauna, flora, and the presence of a favorable climate, confirming the area as a significant fossil Lagerstätte in Southeast Asia. Overall, this study offers a unique snapshot of the past, providing valuable insights into the regional ecosystem and significantly contributing to our understanding of paleoenvironmental conditions and biotic interactions.

An extinct deep-snouted Alligator species from the Quaternary of Thailand and comments on the evolution of crushing dentition in alligatorids

Fossil Alligator remains from Asia are critical for tracing the enigmatic evolutionary origin of the Chinese alligator, Alligator sinensis, the only living representative of Alligatoridae outside the New World. The Asian fossil record is extremely scarce and it remains unknown whether A. sinensis is an anagenetic lineage or alternatively, extinct divergent species were once present. We provide a detailed comparative description of a morphologically highly distinct Alligator skull from the Quaternary of Thailand. Several autapomorphic characters warrant the designation of a new species. Alligator munensis sp. nov. shares obvious derived features with A. sinensis but autapomorphies imply a cladogenetic split, possibly driven by the uplift of the southeastern Tibetan plateau. The presence of enlarged posterior alveoli in Alligator munensis is most consistent with a reversal to the alligatorine ancestral condition of having crushing dentition, a morphology strikingly absent among living alligatorids. Crushing dentition has been previously considered to indicate an ecological specialisation in early alligatorines that was subsequently lost in Alligator spp. However, we argue that there is yet no evidence for crushing dentition reflecting an adaptation for a narrower niche, while opportunistic feeding, including seasonal utilisation of hard-shelled preys, is a reasonable alternative interpretation of its function.

A three-dimensional geometric morphometric analysis of the morphological transformation of Caiman lower jaw during post-hatching ontogeny

Shape ontogenetic changes of the lower jaw in crocodylians are poorly understood. In order to answer some questions related to the inter- and intraspecific morphological variation of the mandible of two extant Caiman species, we performed a three-dimensional geometric morphometric approach. For this purpose, we used landmarks and semilandmarks on two ontogenetic mandibular series of 48 and 15 post-hatching specimens of C. yacare and C. latirostris, respectively. We have also examined the relationship between these anatomical transformations and ontogenetic shifts in diet. We performed a principal component analysis (PCA) for the two species, and regression and partial least squares (PLS) analyses for each species, separately. As a result, species were segregated along the PC1 with specimens of C. yacare showing more gracile mandibles, and specimens of C. latirostris more robust ones. The PC2 and regression analyses showed an age gradient and represented ontogenetic shape changes. Adult caiman mandibles are higher and wider than juvenile ones, and shape changes are more conspicuous in C. latirostris. The PLS analyses showed a significant relationship between shape and diet. Morphological changes of the PLS1 of block-1 match with those of the regression analysis for both species. We have detected morphological transformations in areas where the musculature in charge of mandibular movements is attached. Common morphological changes occurring during ontogeny seem to reflect the same mechanical properties required for crushing and killing in both species, driven by an ontogenetic shift in the diet from invertebrates to vertebrates. Additionally, interspecific differences were also found to be correlated to ontogenetic changes in diet and could be related to dissimilar feeding mechanical requirements (e.g., stiffness and toughness of the item consumed), and to different habitat preferences. Robust mandibles would be more suitable for shallow and fully vegetated environments, as it can be seen in C. latirostris, whereas slender jaws seem to be more suitable for more aquatic species such as C. yacare.

Re-evaluation of the morphology and phylogeny of Diplocynodon levantinicum Huene & Nikoloff, 1963 and the stratigraphic age of the West Maritsa coal field (Upper Thrace Basin, Bulgaria)

Diplocynodon levantinicum Huene & Nikoloff, 1963 was described based on few bone fragments from the West-Maritsa lignite basin of Central Bulgaria. Huene & Nikoloff, 1963 assumed a late Pliocene age, implying that this species represents the stratigraphically youngest crocodilian of Europe. In this current study, we re-evaluate the stratigraphy of the West-Maritsa Basin and conclude a late Oligocene age of ~26 Ma for the Kipra coal-seam, the fossiliferous horizon. Furthermore, topotypical and undescribed D. levantinicum specimens are accessible now and allowed for a deeper taxonomic and phylogenetic analysis. A comparison with other Diplocynodon species reveals D. levantinicum as a valid species, having (1) a long suborbital fenestra, (2) a very short dentary symphysis, (3) a large gap between the first and second dentary alveolus, (4) an occlusion pit in line with the tooth row posterior to the 14^th dentary alveolus, (5) a sulcus lateral to the glenoid fossa and, (6) a lingual foramen for the articular artery situated entirely on the surangular. The phylogenetic analyses find D. levantinicum deeply nested inside the Diplocynodontinae subfamily. After the disappearance of the Paratethyan influence (Solenovian regional stage) in the Upper Thrace Basin this species has roamed during the late Oligocene extensive freshwater lake and swamp ecosystems represented by the Maritsa Formation. Diplocynodon levantinicum represents the only nominal Diplocynodon taxon of late Oligocene (Chattian) age.

A juvenile skull from the early Palaeocene of China extends the appearance of crocodyloids in Asia back by 15–20 million years

The earliest Crocodylia from Asia have been represented so far only by alligatoroids and planocraniids. Although definitive crocodyloids are not known until the late Eocene, it has been hypothesized that Asiatosuchus-like basal crocodyloids originated in Asia before the late Palaeocene. In this paper, we describe a new fossil crocodyloid from the lower Palaeocene of Qianshan Basin, Anhui Province, China. The skull and lower jaw fragment exhibit several characteristics typical of juvenile crocodylians. They also display a combination of features not seen in any other taxon, warranting the erection of a new species and genus, Qianshanosuchus youngi gen. & sp. nov. Its affinities are tested in phylogenetic analyses based on two recent character matrices of Eusuchia. To assess the effect of juvenile characteristics on the outcome of the phylogenetic analyses, juvenile specimens of extant crocodylian taxa are analysed in the same way, showing that the effect of their ontogenetic stage on their placement in the tree is minimal. Our analyses point to a basal crocodyloid position for Q. youngi. With these findings, the presence of Crocodyloidea in Asia is extended to the early Palaeocene, 15–20 Myr earlier than formerly thought. Furthermore, our results corroborate previous hypotheses of a Palaeocene dispersal route of Asiatosuchus-like crocodyloids from Asia into Europe.

Giant dwarf crocodiles from the Miocene of Kenya and crocodylid faunal dynamics in the late Cenozoic of East Africa

We describe two new osteolaemine crocodylids from the Early and early Middle Miocene of Kenya: Kinyang mabokoensis tax. nov. (Maboko, 15 Ma) and Kinyang tchernovi tax. nov. (Karungu and Loperot, 18 Ma). Additional material referable to Kinyang is known from Chianda and Moruorot. The skull was broad and dorsoventrally deep, and the genus can be diagnosed based on the combined presence of a partial overbite, a subdivided fossa for the lateral collateral ligament on the surangular, and a maxilla with no more than 13 alveoli. Phylogenetic analyses based on morphological and combined morphological and molecular data support a referral of Kinyang to Osteolaeminae, and morphological data alone put the new taxon at the base of Euthecodontini. Some Kinyang maxillae preserve blind pits on the medial caviconchal recess wall. Kinyang co‐occurs with the osteolaemine Brochuchus at some localities, and together, they reinforce the phylogenetic disparity between early Neogene osteolaemine‐dominated faunas and faunas dominated by crocodylines beginning in the Late Miocene in the Kenya Rift. The causes of this turnover remain unclear, though changes in prevailing vegetation resulting from tectonic and climatic drivers may provide a partial explanation.

The impact of molecular data on the phylogenetic position of the putative oldest crown crocodilian and the age of the clade

The use of molecular data for living groups is vital for interpreting fossils, especially when morphology-only analyses retrieve problematic phylogenies for living forms. These topological discrepancies impact on the inferred phylogenetic position of many fossil taxa. In Crocodylia, morphology-based phylogenetic inferences differ fundamentally in placing Gavialis basal to all other living forms, whereas molecular data consistently unite it with crocodylids. The Cenomanian Portugalosuchus azenhae was recently described as the oldest crown crocodilian, with affinities to Gavialis, based on morphology-only analyses, thus representing a potentially important new molecular clock calibration. Here, we performed analyses incorporating DNA data into these morphological datasets, using scaffold and supermatrix (total evidence) approaches, in order to evaluate the position of basal crocodylians, including Portugalosuchus. Our analyses incorporating DNA data robustly recovered Portugalosuchus outside Crocodylia (as well as thoracosaurs, planocraniids and Borealosuchus spp.), questioning the status of Portugalosuchus as crown crocodilian and any future use as a node calibration in molecular clock studies. Finally, we discuss the impact of ambiguous fossil calibration and how, with the increasing size of phylogenomic datasets, the molecular scaffold might be an efficient (though imperfect) approximation of more rigorous but demanding supermatrix analyses.

Combined data analysis of fossil and living mammals: a Paleogene sister taxon of Placentalia and the antiquity of Marsupialia

The Cretaceous-Paleogene (KPg) boundary, one of Earth's five major extinction events, occurred just before the appearance of Placentalia in the fossil record. The Gobi Desert, Mongolia and the Western Interior of North America have important fossil mammals occurring just before and after the KPg boundary (e.g. Prodiacodon, Deltatheridium) that have yet to be phylogenetically tested in a character-rich context with molecular data. We present here phylogenetic analyses of >6000 newly scored anatomical observations drawn from six untested fossils and added to the largest existing morphological matrix for mammals. These data are combined with sequence data from 27 nuclear genes. Results show the existence of a new eutherian sister clade to Placentalia, which we name and characterize. The extinct clade Leptictidae is part of this placental sister clade, indicating that the sister clade survived the KPg event to co-exist in ancient ecosystems during the Paleogene radiation of placentals. Analysing the Cretaceous metatherian Deltatheridium in this character-rich context reveals it is a member of Marsupialia, a finding that extends the minimum age of Marsupialia before the KPg boundary. Numerous shared-derived features from multiple anatomical systems support the assignment of Deltatheridium to Marsupialia. Computed tomography scans of exquisite new specimens better document the marsupial-like dental replacement pattern of Deltatheridium. The new placental sister clade has both Asian and North American species, and is ancestrally characterized by shared derived features such as a hind limb modified for saltatorial locomotion.

Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem

First appearing in the latest Cretaceous, Crocodylia is a clade of semi-aquatic, predatory reptiles, defined by the last common ancestor of extant alligators, caimans, crocodiles, and gharials. Despite large strides in resolving crocodylian interrelationships over the last three decades, several outstanding problems persist in crocodylian systematics. Most notably, there has been persistent discordance between morphological and molecular datasets surrounding the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii. Whereas molecular data consistently support a sister taxon relationship, in which they are more closely related to crocodylids than to alligatorids, morphological data indicate that Gavialis is the sister taxon to all other extant crocodylians. Here we present a new morphological dataset for Crocodylia based on a critical reappraisal of published crocodylian character data matrices and extensive firsthand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs scored for 330 characters) and includes a new, illustrated character list with modifications to the construction and scoring of characters, and 46 novel characters. Under a maximum parsimony framework, our analyses robustly recover Gavialis as more closely related to Tomistoma than to other extant crocodylians for the first time based on morphology alone. This result is recovered regardless of the weighting strategy and treatment of quantitative characters. However, analyses using continuous characters and extended implied weighting (with high k-values) produced the most resolved, well-supported, and stratigraphically congruent topologies overall. Resolution of the gharial problem reveals that: (1) several gavialoids lack plesiomorphic features that formerly drew them towards the stem of Crocodylia; and (2) more widespread similarities occur between species traditionally divided into tomistomines and gavialoids, with these interpreted here as homology rather than homoplasy. There remains significant temporal incongruence regarding the inferred divergence timing of the extant gharials, indicating that several putative gavialids ('thoracosaurs') are incorrectly placed and require future re-appraisal. New alligatoroid interrelationships include: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) the recovery of the early Paleogene South American taxon Eocaiman as a 'basal' alligatoroid; and (3) the paraphyly of the Cenozoic European taxon Diplocynodon. Among crocodyloids, notable results include modifications to the taxonomic content of Mekosuchinae, including biogeographic affinities of this clade with latest Cretaceous-early Paleogene Asian crocodyloids. In light of our new results, we provide a comprehensive review of the evolutionary and biogeographic history of Crocodylia, which included multiple instances of transoceanic and continental dispersal.

A new caimanine alligatorid from the Middle Eocene of Southwest Texas and implications for spatial and temporal shifts in Paleogene crocodyliform diversity

Dramatic early Cenozoic climatic shifts resulted in faunal reorganization on a global scale. Among vertebrates, multiple groups of mammals (e.g., adapiform and omomyiform primates, mesonychids, taeniodonts, dichobunid artiodactyls) are well known from the Western Interior of North America in the warm, greenhouse conditions of the early Eocene, but a dramatic drop in the diversity of these groups, along with the introduction of more dry-tolerant taxa, occurred near the Eocene–Oligocene boundary. Crocodyliforms underwent a striking loss of diversity at this time as well. Pre-Uintan crocodyliform assemblages in the central Western Interior are characterized by multiple taxa, whereas Chadronian assemblages are depauperate with only Alligator prenasalis previously known. Crocodyliform diversity through the intervening Uintan and Duchesnean is not well understood. The middle Eocene Devil’s Graveyard Formation (DGF) of southwest Texas provides new data from southern latitudes during that crucial period. A new specimen from the middle member of the DGF (late Uintan–Duchesnean) is the most complete cranial material of an alligatorid known from Paleogene deposits outside the Western Interior. We identify this specimen as a caimanine based on notched descending laminae of the pterygoids posterior to the choanae and long descending processes of the exoccipitals that are in contact with the basioccipital tubera. Unlike Eocaiman cavernensis, the anterior palatine process is rounded rather than quadrangular. The relationships and age of this new taxon support the hypothesis that the modern distribution of caimanines represents a contraction of a more expansive early Cenozoic distribution. We hypothesize that the range of caimanines tracked shifting warm, humid climatic conditions that contracted latitudinally toward the hothouse-icehouse transition later in the Eocene.